#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/halfquatermb";
$geno ="geno.bgl";
$marker ="markers.txt";
$reference ="phased.bgl";
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/quaterquatermb";
$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 62500 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 125000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/quatermb";
#$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 250000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
=head
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/1mb";
$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 1000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/2mb";
$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 2000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/4mb";
$sys = "/usr/bin/perl  /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 4000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr10/halfmb";
$sys = "/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 500000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
=cut
